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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
author abims-sbr
date Wed, 27 Sep 2017 10:01:55 -0400
parents e95d4b20c62d
children 6709645eff5d
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<tool name="Pairwise" id="pairwise" version="2.0">

	<description>
		Run reciproque tblastx pairwise
	</description>

	<macros>
		<import>macros.xml</import>
	</macros>

	<requirements>
		<expand macro="python_required" />
		<requirement type="package" version="2.2.22">blast-legacy</requirement>
		<requirement type="package" version="1.3.1">samtools</requirement>
	</requirements>

  	<command><![CDATA[
        #set $infiles = ""
        #for $input in $inputs
            ln -s '$input' '$input.element_identifier';
            #set $infiles = $infiles + $input.element_identifier + ","
        #end for
        #set $infiles = $infiles[:-1]

        ln -s $__tool_directory__/scripts/S02_xxx_patron_pipeline.sh . &&
        ln -s $__tool_directory__/scripts/S03_run_blast_with_k_filter.sh . &&
        ln -s $__tool_directory__/scripts/S04_run_blast2_with_k_filter.sh . &&
        ln -s $__tool_directory__/scripts/S05_script_extract_match_v20_blastx.py . &&
        ln -s $__tool_directory__/scripts/S06_post_processing_of_pairwise.py . &&
        ln -s $__tool_directory__/scripts/S07_format_match_get_back_nucleotides.py . &&
        ln -s $__tool_directory__/scripts/S08_script_extract_match_v20_blastx.py . &&
        ln -s $__tool_directory__/scripts/S09_post_processing_of_pairwise.py . &&
        ln -s $__tool_directory__/scripts/S10_compare_list_pairs_for_reciprocal_best_hits_test.py . &&
        ln -s $__tool_directory__/scripts/S11_post_processing_of_pairwise.py . &&
        ln -s $__tool_directory__/scripts/S12_prot2dna.py . &&

		python $__tool_directory__/scripts/S01_organize_rbh.py $infiles ${e_value} \${GALAXY_SLOTS:-1}
		> ${output};
  	]]></command>

 	<inputs>
        <param name="inputs" type="data" format="fasta" multiple="true" label="Input files" />
		<param name="e_value" type="float" value="1e-5" label="e_value" help="By default, it's 1e-5. you can write the e-value like this: 1e-5" />
	</inputs>

	<outputs>
		<data format="txt" name="output" label="Pairwise" />
        <collection name="output_fasta_dna" type="list" label="Pairwise DNA">
            <discover_datasets pattern="__name_and_ext__" directory="outputs_dna" />
        </collection>
        <collection name="output_fasta_prot" type="list" label="Pairwise PROT">
            <discover_datasets pattern="__name_and_ext__" directory="outputs_prot" />
        </collection>
	</outputs>

	<tests>
		<test>
            <param name="inputs" ftype="fasta" value="inputs/PfPfiji_Trinity.fasta,inputs/ApApomp_Trinity.fasta,inputs/AmAmphi_Trinity.fasta,inputs/AcAcaud_Trinity.fasta" />
			<param name="e-value" value="1e-5" />
			<output name="output" >
				<assert_contents>
					<has_line line="('PfPfiji_Trinity.fasta', 'ApApomp_Trinity.fasta')"/>
					<has_line line="('PfPfiji_Trinity.fasta', 'AmAmphi_Trinity.fasta')"/>
					<has_line line="('PfPfiji_Trinity.fasta', 'AcAcaud_Trinity.fasta')"/>
					<has_line line="('ApApomp_Trinity.fasta', 'AmAmphi_Trinity.fasta')"/>
					<has_line line="('ApApomp_Trinity.fasta', 'AcAcaud_Trinity.fasta')"/>
					<has_line line="('AmAmphi_Trinity.fasta', 'AcAcaud_Trinity.fasta')"/>

					<has_text text="Number of pairwises parsed = 2" />
					<has_text text="Number of pairwises parsed = 3" />
					<has_text text="Number of pairwises parsed = 0" />
					<has_text text="Number of pairwises parsed = 5" />
					<has_text text="Number of pairwises parsed = 1" />
				</assert_contents>
			</output>
            <output_collection name="output_fasta_prot" type="list">
                <element name="ReciprocalBestHits_AmAmphi_AcAcaud" value="outputs_prot/ReciprocalBestHits_AmAmphi_AcAcaud.fasta" />
                <element name="ReciprocalBestHits_ApApomp_AcAcaud" value="outputs_prot/ReciprocalBestHits_ApApomp_AcAcaud.fasta" />
                <element name="ReciprocalBestHits_ApApomp_AmAmphi" value="outputs_prot/ReciprocalBestHits_ApApomp_AmAmphi.fasta" />
                <element name="ReciprocalBestHits_PfPfiji_AcAcaud" value="outputs_prot/ReciprocalBestHits_PfPfiji_AcAcaud.fasta" />
                <element name="ReciprocalBestHits_PfPfiji_AmAmphi" value="outputs_prot/ReciprocalBestHits_PfPfiji_AmAmphi.fasta" />
                <element name="ReciprocalBestHits_PfPfiji_ApApomp" value="outputs_prot/ReciprocalBestHits_PfPfiji_ApApomp.fasta" />
            </output_collection>
            <output_collection name="output_fasta_dna" type="list">
                <element name="DNAalignment_corresponding_to_protein_from_RBH_AmAmphi_AcAcaud" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_AmAmphi_AcAcaud.fasta" />
                <element name="DNAalignment_corresponding_to_protein_from_RBH_ApApomp_AcAcaud" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_ApApomp_AcAcaud.fasta" />
                <element name="DNAalignment_corresponding_to_protein_from_RBH_ApApomp_AmAmphi" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_ApApomp_AmAmphi.fasta" />
                <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AcAcaud" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AcAcaud.fasta" />
                <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AmAmphi" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AmAmphi.fasta" />
                <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_ApApomp" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_ApApomp.fasta" />
            </output_collection>
		</test>
	</tests>

	<help>

@HELP_AUTHORS@

============
What it does
============

| This tool takes a 'data collection list' containing nucleic fasta sequence files and searches different homologous genes from pairwise comparaisons.
| There are 3 outputs.
|

--------

==========
Parameters
==========

The choice of parameters is possible :

**-e** :
	|  is the option for the choice of the e-value.
	| By default it's 10.
	|

--------

=======
Outputs
=======

This tool, produces the following files :

**Pairwise**:
	| is the general output. It gives the information about what the tool is doing (for each pairwise).
	|

**Pairwise DNA**:
	| is the output wich contains nucleic sequences (of the pairwise) that are homologues. The sequences are with nucleotides. Shows:
	| the name of the query sequence
	| the part of the sequence in nucleotides
	| the name of the match sequence
	| the part of the sequence in nucleotides
	|

**Pairwise PROT**:
	| is the output wich contains proteic sequences (of the pairwise) that are homologues. The sequences are with protein. Shows:
	| the name of the query sequence (the name of the sequence || the position (Start and End) of the homologous sequences || divergence || number of gaps || real divergence || the length of the homologous sequence)
	| the part of the sequence in protein
	| the name of the match sequence (the name of the sequence || the position (Start and End) of the homologous sequences || divergence || number of gaps || real divergence || the length of the homologous sequence)
	| the part of the sequence in protein

--------

===============
Working Example
===============

---------------------------
The input files and options
---------------------------

**Input files**
	| 3 files with 200 nucleic sequences each : Ap.fasta, Ac.fasta et Pp.fasta
	|
**Parameters**
	| e-value = 1e-20
	|

----------------
The output files
----------------

**Pairwise**

| -------------------- Pairwise Pp_Ap --------------------
|
| database :  Pp.fasta
| query file :  Ap.fasta
|
| ***** START run BLAST *****
| ***** END run BLAST *****
|
|
| database :  Ap.fasta
| query file : only the sequences of Pp.fasta who matched during the last BLAST
|
| ***** START run BLAST *****
| ***** END run BLAST *****
|
| [3/5] Get pairs of sequences ...
| Get list of fasta name involved in RBH
| Number of pairwises parsed = 15
| Get subset of Alvinella db
| Get subset of Paralvinella db
|
| -------------------- Pairwise Pp_Ac --------------------
|
| database :  Pp.fasta
| query file :  Ac.fasta
|
| ***** START run BLAST *****
| ***** END run BLAST *****
|
|
| database :  Ac.fasta
| query file : only the sequences of Pp.fasta who matched during the last BLAST
|
| ***** START run BLAST *****
| ***** END run BLAST *****
|
| [3/5] Get pairs of sequences ...
| Get list of fasta name involved in RBH
| Number of pairwises parsed = 13
| Get subset of Alvinella db
| Get subset of Paralvinella db
|
|
| -------------------- Pairwise Ap_Ac --------------------
|
| database :  Ap.fasta
| query file :  Ac.fasta
| 
| ***** START run BLAST *****
| ***** END run BLAST *****
|
|
| database :  Ac.fasta
| query file : only the sequences of Ap.fasta who matched during the last BLAST
|
| ***** START run BLAST *****
| ***** END run BLAST *****
|
| [3/5] Get pairs of sequences ...
| Get list of fasta name involved in RBH
| Number of pairwises parsed = 24
| Get subset of Alvinella db
| Get subset of Paralvinella db
|
|

**Pairwise_output_file_PROT**

| For example the 4 last sequences of the file 19_ReciprocalBestHits_Pp_Ap.fasta
|
| &gt;Ap123_1/1_1.000_748||254...478||[[1/1]][[1/6]]||29.3333333333||0||29.3333333333||75.0
| FVRITVGDEMSRRPKFAMITWVGPEVSPMKRAKVSTDKAFVKQIFQNFAKEIQTSERSELEEEYVRQEVMKAGGA
| &gt;Pp_146_1/2_1.000_713||259...483||[[1/1]][[1/6]]||29.3333333333||0||29.3333333333||75.0
| FAYIRCTNEESKRSKFAMITWIGQGVEAMKRAKVSMDKQFLKEIFQNFAREFQTSEKSELDEVCIKHALAIDDGA
| &gt;Ap66_1/1_1.000_400||192...398||[[1/1]][[1/6]]||21.7391304348||0||21.7391304348||69.0
| LSTSLLNWRKHTLCF*GMKLILIILLISFIIPAILFLLSIFTTMRMPESREKFRPYECGFDPNHSARTP
| &gt;Pp_201_2/2_1.000_691||14...220||[[1/1]][[1/6]]||21.7391304348||0||21.7391304348||69.0
| LSTSLLN*RKQPFASEEMKLLILLLFISALIPRILIILSIFTSIRTPKNREKSSPYECGFDPNHSARTP
|
|

**Pairwise_output_file_DNA**

| For example the 4 last sequences of the file 25_DNAalignement_corresponding_to_protein_from_19_RBH_Pp_Ap.fasta
|
| &gt;Ap123_1/1_1.000_748
| CCAGTAACAAGCCGCCACGGGTCCGTCGTGTCTTCTCTTCAAGGAAAGGTTGACAGATTCTCGTACGCTAGACGTCGCCACCTACTCGTCCTGGACTCCGGTGCCGTAGGTGGCGCCACCTGCTTTCATCACTTCCTGCCTA
| ACGTACTCCTCTTCTAGCTCCGATCTCTCGCTCGTCTGGATCTCTTTGGCAAAGTTCTGGAATATCTGCTTGACGAACGCCTTGTCCGTGCTGACTTTGGCGCGCTTCATTGGGCTCACTTCCGGTCCGACCCACGTGATCA
| TGGCGAACTTCGGTCTTCTGCTCATTTCGTCCCCGACGGTAATACGGACAAAGGCGAACGCCCGCTGGTCATCTTGTAGTTTTGATAACAGATCCTCGTATTCGGTTCCTGTAGAGTCCAGTATAATATTGTCGCCATCATA
| CGTCACAAACGCCCAGTTTGTCTCCGTCGCGTCGCTCCTGACGTCTTCGTAAGCCTGTCCGATAGCCTCTCTGTCGATGTCTGCCATGCTGCTGGTCCCGCTCTCGACGCTAATGAGCCAATCACGACTTCTGACAGACGAG
| TAGACATGCAGACAGCCAGACGGACTGACGGACTGACG
| &gt;Pp_146_1/2_1.000_713
| CATTAATTGTGTGTCTGGTTGTGGGTGTGTGTTATAAGAGACATCACTTAGTGTATACTGATGTCCACGTGGTAGTTGACCAGCATGTCGAATATGGATAGGGACTCGATCTTGAATGGCTATGAGGAGGTTCGCAACGACGA
| CTCGGACATTAACTGGGCTTTCGTAACGTATTCACCTGACAACAAACTAGTACTTGATTCAACTGGCACAGACTACTTCCAGCTCCAGGAGAAATATCAAGATGATATGCGAGGATTTGCTTACATCCGGTGCACTAACGAGG
| AGAGTAAACGTTCTAAATTTGCCATGATTACCTGGATTGGACAAGGAGTGGAAGCAATGAAGCGTGCCAAGGTCAGCATGGACAAACAGTTCCTAAAGGAAATCTTCCAGAATTTCGCAAGAGAATTTCAGACGAGTGAAAAG
| TCAGAGCTTGATGAGGTCTGTATTAAACACGCGCTTGCCATTGACGATGGAGCTGGTTGCAAAGTGGAAAGCGAGGACACGAGAAAAGGGGCCTTTCTCAGGAAAGAGGATGACACTGAAGTGGAAAGGGAAACTAATGTCAA
| CAATGTCTCCGGTGTCGTGGAAGAAGATGATGACGCAAAAAATGCAAATGATTTTAATTACGAAGAGGACTGTAACAATGAATAGGTGCATGTCGATGATTTATATAGAGAACTAGACTTCGCACTCGCTAGGTGGTTGAT
| &gt;Ap66_1/1_1.000_400
| TGATCGTCTTATAAACCTAACTTGAAAAACCTTCCTACCATTTAGGGCTAGCAGCCCTATTAATTATCACACCTATCGCAGCGCTCTCACTATAATTATAAGTATTGCGCCGGGTTTGAACGGATAGCTCTGATGCTGCTAATT
| ACGGGACCTAATAATCCCCAATACTTTATCCTTAGAGAGCTGTACCTCTTAGCACCAGTCTTTTAAACTGGCGAAAGCACACTTTATGCTTCTAAGGAATGAAACTAATTCTTATAATCCTACTAATCTCTTTTATCATCCCCG
| CCATTCTATTTTTACTCTCGATCTTTACTACTATGCGCATGCCAGAGAGCCGTGAAAAATTTAGGCCCTACGAGTGCGGGTTTGACCCCAATCACTCGGCCCGAACCCCATT
| &gt;Pp_201_2/2_1.000_691
| ATCGTAGGGAAAAAGGTGTTCGTGCAGAATGATTGGGGTCAAATCCACATTCGTAGGGGCTAGATTTTTCACGGTTTTTAGGTGTACGAATAGAGGTGAAGATTGATAGGATGATTAAAATTCTTGGGATTAATGCTGAAATAAA
| GAGAAGTAGGATTAAAAGTTTCATTTCCTCAGAAGCAAAGGGTTGCTTTCGTCAGTTTAAAAGACTGGTGCTAAGTAGGTACAGCTCTCTAAGGG

---------------------------------------------------

Changelog
---------

**Version 2.0 - 18/04/2017**

 - NEW: Replace the zip between tools by Dataset Collection


**Version 1.0 - 13/04/2017**

 - TEST: Add funtional test with planemo

 - IMPROVEMENT: Use conda dependencies for blast, samtools and python

    </help>

    <expand macro="citations" />

</tool>